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Wheat DT Rhizosphere SynCom

Community ID CommunityMech:000429
Ecological State ENGINEERED
Environment barley rhizosphere inoculated with wheat-origin SynCom — ontology label: rhizosphere
ENVO:00005801 · HabitatMech ↗
Modeled Environment wheat plant-associated environment — ontology label: plant-associated environment
ENVO:01001001 · HabitatMech ↗

A defined sixteen-strain drought-tolerant bacterial synthetic community assembled from wheat-rhizosphere isolates collected at the Global Change Experimental Facility in Bad Lauchstadt. Rigerte et al. selected isolates with overlapping 16S rDNA sequences to drought- or future-climate-associated amplicon sequence variants, cultured the wheat isolate set on YME agar, combined equal proportions of the sixteen single-strain suspensions, and applied the Wheat DT-SynCom to barley seedlings before Blumeria graminis f. sp. hordei challenge and pre-challenge rhizosphere multi-omics assays.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Buttiauxella sp. W1 — ontology label: Buttiauxella NCBITaxon:82976 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W1 Wheat Wheat Buttiauxella Buttiauxella sp. MK638102"
Pedobacter sp. W2 — ontology label: Pedobacter NCBITaxon:84567 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W2 Wheat Wheat Pedobacter Pedobacter sp. MK638129"
Arthrobacter sp. W3 — ontology label: Arthrobacter NCBITaxon:1663 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W3 Wheat Wheat Arthrobacter Arthrobacter sp. MK638058"
Bacillus sp. W4 — ontology label: Bacillus <firmicutes> NCBITaxon:1386 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W4 Wheat Wheat Bacillus Bacillus sp. MK638067"
Mesorhizobium sp. W5 — ontology label: Mesorhizobium NCBITaxon:68287 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W5 Wheat Wheat Mesorhizobium Mesorhizobium sp. MK638163"
Chitinophaga sp. W6 — ontology label: Chitinophaga NCBITaxon:79328 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W6 Wheat Wheat Chitinophaga Chitinophaga sp. MK638107"
Arthrobacter sp. W7 — ontology label: Arthrobacter NCBITaxon:1663 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W7 Wheat Wheat Arthrobacter Arthrobacter sp. MK638059"
Pseudomonas sp. W8 — ontology label: Pseudomonas NCBITaxon:286 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W8 Wheat Wheat Pseudomonas Pseudomonas sp. MK637939"
Plantibacter sp. W9 — ontology label: Plantibacter NCBITaxon:190323 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W9 Wheat Wheat Plantibacter Plantibacter sp. MK638378"
Pseudomonas sp. W10 — ontology label: Pseudomonas NCBITaxon:286 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W10 Wheat Wheat Pseudomonas Pseudomonas sp. MK637993"
Microbacterium sp. W11 — ontology label: Microbacterium NCBITaxon:33882 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W11 Wheat Wheat Microbacterium Microbacterium sp. MK638191"
Inquilinus sp. W12 — ontology label: Inquilinus NCBITaxon:171673 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W12 Wheat Wheat Inquilinus Inquilinus sp. MK638140"
Variovorax sp. W13 — ontology label: Variovorax NCBITaxon:34072 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W13 Wheat Wheat Variovorax Variovorax sp. MK638657"
Streptomyces sp. W14 — ontology label: Streptomyces NCBITaxon:1883 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W14 Wheat Wheat Streptomyces Streptomyces sp. MK638538"
Phyllobacterium sp. W15 — ontology label: Phyllobacterium NCBITaxon:28100 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W15 Wheat Wheat Phyllobacterium Phyllobacterium sp. MK638310"
Ensifer sp. W16 — ontology label: Ensifer NCBITaxon:106591 · TaxonMech · TraitMech DOMINANT
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "W16 Wheat Wheat Ensifer Ensifer sp. MK638128"

Ecological Interactions

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

Ecological interaction network for Wheat DT Rhizosphere SynCom Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Other

Wheat DT-SynCom powdery mildew resistance

The wheat-origin, 16-member DT-SynCom reduced barley leaf powdery-mildew DAF fluorescence by 43.3% relative to mock treatment after Blumeria graminis f. sp. hordei challenge. All three inoculants protected plants; their pairwise differences were not significant. This supports ISR-like protection but does not assign necessity to JA, ethylene or SA signaling. PEG-tolerant isolate selection is not a test of whole-plant drought protection.

Evidence

  • PMID:42453107 - SUPPORT (IN_VIVO)
    "Mean fluorescence was reduced by 50.4% in the barley SynCom treatment, 43.3% in the wheat SynCom treatment, and 34.9% in the WCS417r treatment, relative to the mock treatment. "
  • PMID:42453107 - SUPPORT (IN_VIVO)
    "These results demonstrate that both the barley and wheat SynComs induce ISR in a manner similar to that of the ISR-eliciting bacterium WCS417r. "

Wheat DT-SynCom selective rhizosphere functional shifts

Before pathogen challenge, the wheat DT-SynCom treatment produced selective changes in measured barley-rhizosphere RNA features, including downregulation of PF02868, PF01614 and K05516. Overall functional profiles and bacterial community structure showed no significant treatment shift. These are metatranscriptomic observations, not PICRUSt predictions. Similarity-based contig annotations do not attribute transcripts to individual inoculant strains, and no perturbation establishes these changes as necessary mediators of the later disease-protection outcome.

Evidence

  • PMID:42453107 - SUPPORT (IN_VIVO)
    "Inoculation with wheat SynCom resulted in downregulation of PF02868, PF01614 (PFAM; IclR-family transcriptional regulator, C-terminal domain), and K05516 (KEGG; stress-induced DnaJ-like molecular chaperone) "
  • PMID:42453107 - SUPPORT (IN_VIVO)
    "Overall, bioinoculants induced selective, function-specific shifts in rhizosphere microbial gene expression, not broad community changes. "
  • PMID:42453107 - SUPPORT (IN_VIVO)
    "The metatranscriptomic contigs were assigned based on sequence similarity (not reference SynCom genomes)"

Associated Datasets

Dataset Type Repository Accession
Wheat DT-SynCom rhizosphere multi-omics BioProject PRJNA1405459
NCBI BioProject accession reported for the barley rhizosphere 16S rRNA gene amplicon, rhizosphere metatranscriptome, and host leaf RNA-seq data generated in the DT-SynCom powdery mildew resistance study. 		MULTI_OMICS NCBI_BIOPROJECT PRJNA1405459

Knowledge gaps & discussions (2)

KNOWLEDGE_GAP OPEN When will BioProject PRJNA1405459 resolve publicly at NCBI?

The paper reports PRJNA1405459 for the generated sequencing data, but NCBI BioProject returned a "not public" placeholder for accession 1405459 during curation on 2026-09-24.

Attaches to: associated_datasets#PRJNA1405459

KNOWLEDGE_GAP OPEN Which pre-infection responses mediate wheat DT-SynCom disease protection in barley?

Molecular samples preceded the pathogen assay, so these profiles cannot be described as post-infection responses. No significant pairwise difference establishes a superior inoculant. The authors could not assign ISR to specific hormone pathways. OTU matches at 99% identity suggest persistence of related taxa, not unique viable-strain identification. Preserve the prior selective-versus-broad correction and the dated BioProject-visibility discussion.

Attaches to: ecological_interactions#Wheat DT-SynCom powdery mildew resistance, ecological_interactions#Wheat DT-SynCom selective rhizosphere functional shifts

2 evidence item(s)
PMID:42453107

Although our data did not allow direct assignment of ISR to specific JA-, ET-, or SA-dependent pathways

PMID:42453107

Although strain-level identity cannot be confirmed by 16S rRNA gene-based identification alone

External Resources

Name Repository Resource ID
Primary publication - barley and wheat DT-SynComs
Frontiers in Microbiology 2026 open-access primary article, PMID:42453107 and PMCID:PMC13365038, describing barley- and wheat-origin DT-SynComs for barley powdery mildew resistance. 		OTHER doi:10.3389/fmicb.2026.1818676
  • PMID:42453107 - SUPPORT (OTHER)
    "Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community "

Environmental Factors

Factor Value Unit
GCEF wheat isolate source Wheat cultivar RGT Reform rhizosphere N/A
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "The strains were isolated from the rhizospheres of the barley cultivar “Antonella” and the wheat cultivar “RGT Reform” "
Equal-proportion wheat strain mixture 16 strains in 10 mM MgCl2 N/A
  • PMID:42453107 - SUPPORT (IN_VITRO)
    "The barley strains were combined in equal proportions into a synthetic community and the wheat strains into a separate community "
Barley powdery mildew challenge Blumeria graminis f. sp. hordei N/A
  • PMID:42453107 - SUPPORT (IN_VIVO)
    "Plants were then grown for one week as described before to allow fungal structures to develop, after which leaves were harvested and infection intensity was evaluated by fluorescence-based quantification of fungal structures following DAF staining "

Growth Media

Pikovskaya agar rhizobacteria isolation

Temperature 25 C

Preparation notes: Used to isolate phosphate-solubilizing barley and wheat rhizobacteria from GCEF rhizosphere soil before DT-SynCom strain selection.

Evidence

PMID:42453107

"a suspension was inoculated on Pikovskaya’s (1948) agar medium. Plates were then incubated for three weeks at 25 °C and colonies showing phosphate solubilization (observed as clear halos around them) were purified. "

YME agar DT-SynCom preparation

Temperature 25 C

Preparation notes: The barley and wheat SynCom strains were cultivated on yeast malt extract agar before resuspension, OD600 normalization, pelleting, and equal-proportion mixing.

Evidence

PMID:42453107

"Bacterial strains from the rhizosphere of barley and wheat were cultivated for three days at 25 °C on yeast malt extract (YME) agar. "

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: barley rhizosphere inoculated with wheat-origin SynCom ↗ TaxonMech: Buttiauxella sp. W1 ↗ TraitMech: Buttiauxella sp. W1 ↗ TaxonMech: Pedobacter sp. W2 ↗ TraitMech: Pedobacter sp. W2 ↗ TaxonMech: Arthrobacter sp. W3 ↗ TraitMech: Arthrobacter sp. W3 ↗ TaxonMech: Bacillus sp. W4 ↗ TraitMech: Bacillus sp. W4 ↗ TaxonMech: Mesorhizobium sp. W5 ↗ TraitMech: Mesorhizobium sp. W5 ↗ TaxonMech: Chitinophaga sp. W6 ↗ TraitMech: Chitinophaga sp. W6 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗